Missions

The objective of the post-doctoral fellowship is to quantify and understand the relative roles of the environment, colonization history and selection pressures related to the different phases of invasion on the distribution of genomic variability in raccoon (Procyon lotor) populations in France. Human-induced biological invasions are one of the four major causes of biodiversity loss. Understanding biological invasions to better control them has become critical to mitigate the 6th mass extinction. The tools used are multiple, from occurrence and range evolution data in new environments to the massive use of molecular data for phylogeographic reconstruction of populations. On this last point, invasive populations inherently show low diversity related to the founder effect, especially when the original population is unique resulting in a single introduction. This low diversity makes it more difficult to conduct fine spatial scale studies and to understand precisely the mechanisms of invasion during the first phases of introduction and expansion. For this reason, conservation biology and in particular invasion biology has recently entered the era of population genomics. These genomic aspects of biological invasion offer unprecedented power to reconstruct invasion dynamics but also to understand the evolutionary aspects of invasion, i.e. which genes are under selection in the different phases of invasion, what is the adaptive potential of species in the new environment ... etc. Recent advances in genomics associated with the development of increasingly accurate geographic information systems are leading to large-scale genomic and environmental data that allow the combination of population genomics, landscape ecology, modelling of species distribution and gene flow in a recent discipline: landscape genomics, which is increasingly useful for understanding biological invasions.
In this project, it is proposed to implement a landscape genomics approach on French raccoon populations (Procyon lotor). The raccoon has been present in France since the middle of the 20th century and is currently established in three viable and expanding populations (i.e. with reproduction in the wild and distribution areas continuing to increase): the population of the North-East of France, the oldest, well established, the population of the Massif Central, established since the beginning of the 1990's, and finally, the population of Gironde, which is more recent as it dates back to the beginning of the 2010s. The Gironde population has been monitored since the first detections in the wild and samples cover the entire process of installation and the beginning of colonization in time and space. This monitoring offers an exceptional opportunity to reconstruct the pathways of invasion of the raccoon from installation to the first phases of expansion. We therefore propose to implement this landscape genomics approach applied to the Gironde population as a first step. High-throughput genomic data will be obtained by ddRadSeq sequencing to obtain between 10,000 and 100,000 SNP markers offering essential power for the demo-genetic reconstruction of the installation and expansion of the raccoon in this region.
The person recruited will have to valorise, in the form of scientific publications in international journals, the data obtained in response to the applied and fundamental questions of the project's supervisory team.

Activités

The candidate will take the lead in developing the relevant scientific questions and in selecting and implementing analytical approaches of genotypes. The candidate will seek to address all or parts of the following issues:
- Understand which elements of the landscape ensure the functional connectivity of populations by investigating associations between gene flow and habitat type. Understanding which landscape features facilitate raccoon movement will allow for the development of trapping strategies that are more appropriate to the actual movements of the animals. Functional connectivity corridors could also be determined to anticipate the connection routes between this population in Gironde and that of the Massif Central.
- Reconstructing the kinship structures of the Gironde population with high-throughput genomic markers in order to estimate the population size by recent genetic CMR approaches. A comparison with other approaches will be made in order to better identify the best tools for monitoring population size variation and the effectiveness of management measures.
- Identify the pattern of genes under selection by taking advantage of the raccoon reference genome. It is noted that a comparative approach with the 2 other large populations in France is expected for this last theme.

Compétences

- Extensive knowledge of population genetics and genomics;
- Knowledge of / interest in carnivorous mammal ecology, invasion biology, conservation biology ;
- Knowledge of / interest in wildlife management and finalized scientific questions;
- Proficiency in bioinformatics required to process raw high-throughput sequencing data (possibly ddRadSeq)
- Knowledge of landscape genetics and genomics methodologies;
- Ability to work actively in collaboration with local and remote partners;
- Autonomy in data management and analysis;
- Proficiency in English (level C1 of the European Framework of Reference for Languages) and demonstrated writing skills in English (production of scientific articles);
- Ability to present results to a non-scientific audience / biodiversity managers;

Contexte de travail

The host lab is the Biometry and Evolutionary Biology Lab (LBBE, UMR CNRS 5558: https://lbbe.univ-lyon1.fr/) from the University of Lyon 1, CNRS and VetAgroSup, located in the outskirt of Lyon, France. Almost 200 people contribute to the research at the LBBE that brings together mathematical modelling and IT to answers questions in ecological, evolutionary and health (humans, animals) sciences. The LBBE is among the most important ecology lab in France, with a long history of scientific collaborations s with partners in charge of studies and research on wildlife such as the French Office for Biodiversity and with wildlife managers (national park services, Game and Wildlife services).

The post-doc will work in close collaboration with Jean-François Maillard (French Office for Biodiversity, Species Conservation and Management Service), and Sébastien DEVILLARD (Ecology and Evolution of populations Team at the LBBE).
Our little extras :
- A stimulating work environment in contact with research staff
- Professional support with in-house training
- The possibility of teleworking
- A company restaurant where you can have lunch at an attractive price.
- Partial reimbursement of travel expenses (75%)
+ sustainable mobility package of up to €300/year
- A site accessible by public transport (Tram T1 + T4 + bus)
- 44 days vacation / RTT per year
- Financial contribution to health insurance costs